梅花草属叶绿体基因组进化分析

叶绿体基因组序列变异和基因组成等特征可有效反映植物类群间的系统发育和进化关系。本研究利用Illumina高通量测序平台对梅花草属（Parnassia）及其近缘属5种植物的叶绿体基因组进行测序和组装,同时基于已发表的近缘种叶绿体基因组信息,对梅花草属叶绿体基因组结构特征、序列遗传变异和蛋白编码基因密码子偏好性比对分析。结果显示：梅花草属叶绿体基因组整体结构较为保守,均为四分体结构;梅花草多个基因出现假基因化,而本属其他物种叶绿体基因组成一致,均编码115个基因;与近缘属物种相比,本属所有物种均丢失rpl16基因的内含子;蛋白质编码基因的非同义/同义替代率比值较低,叶绿体基因可能经历纯化选择作用;密码子偏好性聚类结果与蛋白编码序列重建的系统发育关系结果一致。本研究表明选择压力可能在梅花草属叶绿体基因组蛋白编码基因进化过程中发挥作用,有助于进一步理解梅花草属植物的进化和适应机制。     

丝兰属6种植物叶绿体基因组特征分析

为了理清丝兰属（Yucca）叶绿体基因组特征和序列变异情况,进行丝兰属植物叶绿体比较基因组学分析,并构建基于叶绿体基因组的系统发育树。利用高通量测序技术获得无刺龙舌兰（Y. treculeana）叶绿体基因组序列,结合丝兰属现已发表的叶绿体基因组,使用生物信息学方法对6种丝兰属植物叶绿体全基因组进行基本结构、重复序列、边界收缩与扩张以及序列变异分析等在内的比较基因组学研究,并进行系统发育分析。结果表明：6种丝兰属植物叶绿体基因组大小、基因的类型及数目相近,种间基因组结构比较保守;从丝兰属植物叶绿体基因组中检测到多条重复序列,其中SSR位点多是由单核苷酸、双核苷酸和四核苷酸组成,且偏好使用A、T碱基;根据核酸多态性指数π≥0.008,在6种丝兰属植物叶绿体基因组中筛选出了psbK-psbl-trnS-GCU、rpl20-rps12和ccsA-ndhD 3个高变异区域;基于叶绿体全基因组和LSC+SSC区序列构建的系统发育关系基本一致,确定了6种丝兰属植物间的系统发育关系,其中无刺龙舌兰与克雷塔罗丝兰（Y. queretaroensis）的亲缘关系最近。本研究测序获得了无刺龙舌兰叶绿体基因组,揭示了6种丝兰属植物叶绿体基因组特征和序列变异情况,明确了各物种间的亲缘关系,研究结果可为后续丝兰属植物分子标记开发及系统发育研究提供参考。     

Complete Sequencing of Five Araliaceae Chloroplast Genomes and the Phylogenetic Implications

Background

The ginseng family (Araliaceae) includes a number of economically important plant species. Previously phylogenetic studies circumscribed three major clades within the core ginseng plant family, yet the internal relationships of each major group have been poorly resolved perhaps due to rapid radiation of these lineages. Recent studies have shown that phyogenomics based on chloroplast genomes provides a viable way to resolve complex relationships.

Methodology/Principal Findings

We report the complete nucleotide sequences of five Araliaceae chloroplast genomes using next-generation sequencing technology. The five chloroplast genomes are 156,333–156,459 bp in length including a pair of inverted repeats (25,551–26,108 bp) separated by the large single-copy (86,028–86,566 bp) and small single-copy (18,021–19,117 bp) regions. Each chloroplast genome contains the same 114 unique genes consisting of 30 transfer RNA genes, four ribosomal RNA genes, and 80 protein coding genes. Gene size, content, and order, AT content, and IR/SC boundary structure are similar among all Araliaceae chloroplast genomes. A total of 140 repeats were identified in the five chloroplast genomes with palindromic repeat as the most common type. Phylogenomic analyses using parsimony, likelihood, and Bayesian inference based on the complete chloroplast genomes strongly supported the monophyly of the Asian Palmate group and the Aralia-Panax group. Furthermore, the relationships among the sampled taxa within the Asian Palmate group were well resolved. Twenty-six DNA markers with the percentage of variable sites higher than 5% were identified, which may be useful for phylogenetic studies of Araliaceae.

Conclusion

The chloroplast genomes of Araliaceae are highly conserved in all aspects of genome features. The large-scale phylogenomic data based on the complete chloroplast DNA sequences is shown to be effective for the phylogenetic reconstruction of Araliaceae.     

壳斗科植物叶绿体基因组结构及变异分析

利用生物信息学方法比较壳斗科6个属14个物种的叶绿体基因组间差异,以近缘物种榛为外类群构建系统进化树,揭示壳斗科叶绿体基因组的结构特征及变异规律。结果显示,14种壳斗科植物的叶绿体基因组均为双链环状分子结构,大小在160 kB左右,差异较小,最大仅差1 366 bp;基因顺序基本一致,而基因数量有所差异,infA、petG、rpl22、ycf1、ycf15等多个基因在部分物种中发生丢失;主要有32个蛋白编码基因长度发生变异,其原因是内含子的丢失、内含子或者编码区的长度改变,华南锥基因长度变异较大;4个IR边界相对保守,但锥栗、Castanea pumila、华南锥3个物种由于边界扩张导致rps19基因部分序列进入到IR区;以榛为外类群构建的系统发育树,各进化支支持率较高,分辨率较好。研究结果表明,叶绿体基因组可以用于分析关系较近与进化较快物种的系统发生问题,为系统发育和进化研究提供依据。     

极小种群濒危植物广西火桐、丹霞梧桐的叶绿体基因组特征

广西火桐(Firmiana kwangsiensis)和丹霞梧桐(F. danxiaensis)是我国南方特有物种, 其分布范围狭窄, 种群数量少。为了解其叶绿体基因组结构及系统发生关系, 本文通过高通量测序方法获得广西火桐和丹霞梧桐的浅层基因组数据, 通过生物信息学方法对叶绿体全基因组进行组装, 并对其结构特征进行分析。结果表明: 广西火桐和丹霞梧桐的叶绿体基因组大小分别为160,836 bp和161,253 bp, 具有典型被子植物叶绿体基因组环状四分体结构, 包含长度分别为89,700 bp、90,142 bp的大单拷贝区(large single copy, LSC), 长度分别为19,970 bp、20,067 bp的小单拷贝区(small single copy, SSC)及长度分别为25,583 bp、25,522 bp的2个反向重复序列区(inverted repeat sequence, IR)。两个物种的叶绿体基因组共注释得到131个基因, 包括86个蛋白编码基因、37个tRNA基因和8个rRNA基因。广西火桐的叶绿体基因组中共检测出26个正向重复序列、2个反向重复序列、21个回文重复序列、21个串联重复序列和98个简单重复序列; 丹霞梧桐叶绿体基因组中共检测出23个正向重复序列、5个反向重复序列、21个回文重复序列、30个串联重复序列和107个简单重复序列。系统发生分析结果表明5种梧桐属(Firmiana)植物构成两个强烈支持的分支(支持率100%), 一个分支为广西火桐、美丽火桐(F. pulcherrima)和火桐(F. colorata), 其中广西火桐与美丽火桐构成姐妹群; 另一分支是互为姐妹群的丹霞梧桐和云南梧桐(F. major)。综上所述, 广西火桐和丹霞梧桐的叶绿体基因组结构、基因排列及重复序列具有较高的相似性, 系统进化树将5种梧桐属物种分为两个分支, 其中广西火桐和美丽火桐最近; 而丹霞梧桐与云南梧桐关系最近。本研究鉴定的SSR位点可为梧桐属物种系统发生、进化关系的研究提供遗传信息。     

西北干旱区孑遗濒危植物四合木(Tetraena mongolica)叶绿体基因组特征研究及比较分析

四合木(Tetraena mongolica)是我国特有的蒺藜科(Zygophyllaceae)强旱生小灌木,因其起源古老、抗逆性强,所以可作为生物多样性起源和环境演变研究的理想对象,具有重要的学术研究价值。本研究采用Illumina双末端测序技术对四合木叶绿体基因组进行建库测序和分析。选取蒺藜目及牻牛儿苗目共计30个物种叶绿体基因组,与四合木进行系统发育关系分析探讨。结果表明:四合木叶绿体基因组长度为106259bp,其中反向重复区(IR区中)有7种基因,包括4种PCG基因,3种tRNA基因。叶绿体基因组共编码98种基因,包括65种蛋白编码基因、29种tRNA基因与4种rRNA基因。生物信息学表明,在四合木中共搜到92个SSR位点,其中包括74个单核苷酸重复基序,7个二核苷酸重复基序,1个三核苷酸重复基序,9个四核苷酸重复基序和1个五核苷酸基序。没有发现六核苷酸,其中单核苷酸重复在四合木的叶绿体基因组SSR中占比为80.1%。通过MEGA软件采用近邻结合法(neighbor-joining,NJ)对四合木等31个物种的叶绿体基因组进行聚类分析,发现四合木与蒺藜科三齿拉雷亚灌木为最近的姐妹种,其次为牻牛儿苗科智利白桦植物亲缘关系较近,与牻牛儿苗科天竺葵属和牻牛儿苗科高桂花属亲缘关系最远,说明四合木属于蒺藜科物种,这对于四合木的研究等具有一定的参考价值。     

Phylogenetic relationships and the maternal donor of Roegneria (Triticeae: Poaceae) based on three nuclear DNA sequences (ITS,Acc1, and Pgk1) and one chloroplast region (trnL-F)

Roegneria is a polyploid perennial genus in the tribe Triticeae. Some species of Roegneria are morphologically similar to genus Elymus and have been classified in Elymus. To investigate the delimitation and phylogenetic relationships of Roegneria, nuclear (ITS, Acc1, and Pgk1) and chloroplast (trnL–trnF) DNA regions were sequenced for 38 allopolyploid species and 32 diploid species of Triticeae. Phylogenetic analyses of nuclear DNA revealed that all Roegneria species were included in the St and Y genome clades, and that the Y genome was closely related to the V and Xp genomes. The chloroplast DNA dataset showed that Roegneria species were grouped with Pseudoroegneria species. The Pseudoroegneria species from the Middle East (P. libanotica and P. tauri) and Central Asia (P. strigosa) were more closely related to Roegneria species. The results suggested that: (i) the species containing the St and Y genomes should be segregated from Elymus and treated as a distinct genus, Roegneria, based on the genomic constitution; (ii) P. libanotica, P. tauri, and/or P. strigosa potentially served as the maternal donor of the St genome in Roegneria; (iii) The Y genome of Roegneria originated from a diploid Y genome species, and the V and Xp genomes may have contributed to Y genome formation; (iv) among Roegneria species of previously uncertain genomic constitution, R. seriotina was tetraploid and possessed the StY genomes, E. calcicolus was hexaploid with the StYH genomic constitution and should be classified in Campeiostachys, R. glaucifolia possessed the StStY genomes, and R. tschimganica had the genomic constitution St₁St₂Y.     

孑遗濒危植物矮扁桃叶绿体全基因组特征分析及亲缘关系鉴定

对第三纪孑遗濒危植物矮扁桃（Amygdalus nana）叶绿体全基因组进行结构特征分析,并探究其与近缘物种之间的系统进化关系。利用Illumina HiSeq Xten测序技术获取叶绿体全基因组序列,对其进行组装、注释和特征分析。结果表明：①矮扁桃叶绿体全基因组总长度为158 596 bp,其中LSC长度为86 771 bp,SSC长度为19 037 bp,2个IRs均为26 394 bp,为环状四分体结构。共注释130个基因,包括85个PCGs、37个tRNA和8个rRNA。②对6种植物进行IR边界区扩张和收缩分析,发现在4个边界区的基因类型和基因分布情况存在一定差异,并且亲缘关系越紧密差异程度越小。③在矮扁桃叶绿体全基因组中共预测了71个SSRs位点。④系统发育分析结果显示,在扁桃亚属中,矮扁桃在亲缘关系上与蒙古扁桃更近,而与长柄扁桃和榆叶梅的亲缘关系稍远。本研究对矮扁桃叶绿体全基因组进行了深度剖析,并且涉及大量被子植物的叶绿体全基因组资料,为桃属植物之间的进化关系和植物鉴定提供参考依据。     

鲁桑叶绿体基因组序列及特征分析

鲁桑(Morus multicaulis)是亚洲地区栽培的重要经济作物。以鲁桑品种日本胡橙为实验材料, 利用高通量测序技术对鲁桑叶绿体基因组进行测序, 获得NCBI登录号(KU355297), 并研究鲁桑的叶绿体基因组结构。结合前人对蒙桑(M. mongolica)、印度桑(M. indica)和川桑(M. notabilis)的研究结果, 对鲁桑的系统进化关系进行了探讨。研究结果表明: 鲁桑叶绿体基因组是一个典型的四部分结构, 全长159 154 bp, 共注释130个基因, 包含85个蛋白质编码基因(18个基因在反向重复区重复)、37个转运RNA (tRNA)基因和8个核糖体RNA (rRNA)基因。生物信息学分析表明, 在鲁桑中共搜索到82个SSR位点, 单核苷酸、二核苷酸、三核苷酸、四核苷酸和五核苷酸重复基序个数分别为63、7、2、9和1个, 并没有发现六核苷酸; 其中单核苷酸重复在鲁桑的叶绿体基因组SSR中占76.8%。采用MEGA 6.0软件, 通过最大似然法和近邻结合法对包括4个桑属物种在内的15个物种的叶绿体基因组序列进行聚类分析, 2种方法得到的聚类结果均为鲁桑和蒙桑聚在一起。研究结果对叶绿体基因组工程研究及桑属种间的分子标记开发和优良品种培育具有一定的参考价值。     

朱砂根叶绿体全基因组解析及系统发育分析

基于Illumina平台对朱砂根和红凉伞叶绿体全基因组进行测序,利用生物信息学比较叶绿体基因组结构特征与变异程度,旨在明确朱砂根（Ardisia crenata）及红凉伞（Ardisia crenata var. bicolor）叶绿体基因组特征及差异,并与同科其他物种叶绿体全基因组进行比较分析,确定其在紫金牛属系统发育位置。结果表明,朱砂根和红凉伞均为由一个大单拷贝区（LSC）、一个小单拷贝区（SSC）和一对反向重复区（IRa/IRb）构成的环状四分体结构,注释得到132个基因,其重复序列的类型与分布模式相似,但数量有所差异。其中psbA、matK、rpoC2、ropB、ndhK、accD、ndhF、ndhD、ndhH及ycf1等基因的编码区存在差异,这些位点为朱砂根分子鉴定提供新位点。朱砂根及红凉伞叶绿体基因组具有较高保守性,叶绿体基因组之间没有重排或倒置,IR区序列变异最低,SSC区变异程度最高。系统发育树分析表明紫金牛科和报春花科为两个分支,朱砂根和红凉伞归为紫金牛科,且朱砂根与红凉伞亲缘关系最为密切,从分子水平为红凉伞作为朱砂根变种提供了科学解释。本研究解析了朱砂根及变种红凉伞叶绿体基因组结构,探讨了紫金牛科属间系统发育关系,也为紫金牛科药用植物分类鉴定、系统进化及资源开发利用研究奠定基础。     

Endo-allopolyploidy of autopolyploids and recurrent hybridization—A possible mechanism to explain the unresolved Y-genome donor in polyploid Elymus species (Triticeae: Poaceae)

The genus Elymus L. in the tribe Triticeae (Poaceae) includes economically and ecologically important forage grasses. The genus contains the pivotal St genome from Pseudoroegneria in combination with other genomes in the tribe. Many Elymus species are tetraploids containing the StY genomes. It is thought that polyploidization characterizes the speciation of the genus in which the Y is considered as another key genome. Based on data from cytological, genome in situ hybridization, and molecular studies, we hypothesized an endo-allopolyploidy origin of the StY-genome species from the autotetraploid Pseudoroegneria species. To test this hypothesis, we amplified, cloned, and sequenced five single-copy nuclear genes (i.e., alcohol dehydrogenase 1–3, Adh1–Adh3, RNA polymerase II, Rpb2; and Waxy) from Elymus, Pseudoroegneria, and Hordeum species. The phylogenetic trees constructed based on the sequencing analyses of all genes indicated that diploid and autotetraploid Pseudoroegneria species were closely related, although with considerable genetic variation in tetraploids. In addition, the StY-genome Elymus species tended to have a close relationship with the diploid and autotetraploid Pseudoroegneria species, although different phylogenetic relationships among the gene trees were detected. These results indicated that the StY-genome species may have an autotetraploid origin and experienced recurrent hybridization. The complex St genomes in Pseudoroegneria in the polyploid state may gain more opportunities for within-species differentiation and recurrent hybridization. As a result, series modified versions of St genomes evolved into the StY genomes in some Elymus species.     

青藏高原特有种-藏扇穗茅叶绿体基因组测序及序列分析

藏扇穗茅（Littledalea tibetica）是禾本科（Poaceae）雀麦族（Bromeae）中一个具有重要生态价值的多年生高山特有种,主要分布于青藏高原及其毗邻地区。本文采用基于第二代高通量测序平台的Illumina MiSeq技术,对青藏高原特有种—藏扇穗茅进行了叶绿体基因组测序,首次建立了雀麦族物种的标准测序流程;同时,以其近缘物种—黑麦草（Lolium perenne）的叶绿体基因组序列作为参考,组装获得它的叶绿体基因组序列。结果表明,藏扇穗茅叶绿体基因组序列全长136 852 bp,GC含量为38.5%,呈典型的四段式结构,其中大（LSC）、小（SSC）单拷贝区大小分别为80 970和12 876 bp,反向互补重复区（IR）大小为21 503 bp,共注释得到141个基因,包含95个蛋白编码基因、38个tRNA基因和8个rRNA基因,主要分布于大单拷贝区和小单拷贝区。同时,基于藏扇穗茅和其它30种禾本科植物叶绿体基因全序列构建的系统发育树显示,藏扇穗茅与早熟禾亚科中小麦族植物亲缘关系较近。     

毛茛科和芍药科叶绿体基因组密码子特征和系统发育比较

为研究和比较毛茛科和芍药科叶绿体基因组密码子使用模式和系统进化关系,以完成测序的毛茛科33种植物、芍药科7种植物叶绿体基因组为材料,采用分析软件CodonW在线软件CUSP和R软件对叶绿体基因进行密码子特征分析。用MAFFT 软件,MEGA软件进行系统发育分析。研究结果表明芍药科植物叶绿体基因组和毛茛科植物（耧斗菜属除外）叶绿体基因组高频密码子一致性高,具有29个高频密码子,基本偏向与于A/U结尾,但最优密码子存在差异。毛茛科和芍药科叶绿体基因组密码子偏好性的形成因素主要受自然选择的影响,且芍药科叶绿体基因组密码子偏好性受自然选择的影响大于毛茛科。基于叶绿体基因组全序列和基于叶绿体基因组CDS序列的系统进化关系表明,芍药科基于叶绿体基因组全序列和基于叶绿体基因组CDS序列的系统进化关系虽然部分不同,但都可以被划分为芍药组和牡丹组。毛茛科基于叶绿体基因组的系统进化关系不符合中国植物志分类关系,但支持把毛茛科划分为4亚科14族。系统进化分析结果也支持芍药科独立于毛茛科和毛茛目,被划分到虎耳草目,同时证明了叶绿体基因组作为超级DNA条形码的可行性。     

白花刺续断野生居群的叶绿体全基因组特征解析

白花刺续断在中国西藏是一种常用的药用植物,但其叶绿体全基因组的相关研究较少。为揭示该物种叶绿体全基因组的基本特征并探讨其谱系遗传结构,该研究利用Illumina测序平台对来自5个野生居群的10个白花刺续断个体进行二代测序,经组装、注释,得到10条完整的叶绿体全基因组序列,并对它们的基因组特征和居群间的谱系进化关系进行了初步研究。结果表明:(1)白花刺续断的叶绿体全基因组大小为155 335～156 266 bp,共注释113个基因,包括72个蛋白编码基因、30个tRNA基因和4个rRNA基因,其叶绿体基因组的大小、结构、GC含量及基因组成等方面在种内高度保守。(2)基因组比较分析表明,白花刺续断变异较大的片段均位于单拷贝区,且IR边界未出现明显的扩张和收缩。(3)群体遗传分析发现,白花刺续断的野生居群具有明显的地理遗传结构,不同居群间在遗传距离与地理距离上具有一定的相关性。研究认为,白花刺续断叶绿体基因组在种内居群水平上比较保守,且叶绿体基因组可在居群水平上揭示物种的地理遗传结构。这为后续开展刺续断属物种群体遗传学和系统发育基因组学研究奠定了基础。     

Phylogenetic analysis of Oryza species, based on simple sequence repeats and their flanking nucleotide sequences from the mitochondrial and chloroplast genomes

Simple sequence repeats (SSR) and their flanking regions in the mitochondrial and chloroplast genomes were sequenced in order to reveal DNA sequence variation. This information was used to gain new insights into phylogenetic relationships among species in the genus Oryza. Seven mitochondrial and five chloroplast SSR loci equal to or longer than ten mononucleotide repeats were chosen from known rice mitochondrial and chloroplast genome sequences. A total of 50 accessions of Oryza that represented six different diploid genomes and three different allopolyploid genomes of Oryza species were analyzed. Many base substitutions and deletions/insertions were identified in the SSR loci as well as their flanking regions. Of mononucleotide SSR, G (or C) repeats were more variable than A (or T) repeats. Results obtained by chloroplast and mitochondrial SSR analyses showed similar phylogenetic relationships among species, although chloroplast SSR were more informative because of their higher sequence diversity. The CC genome is suggested to be the maternal parent for the two BBCC genome species (O. punctata and O. minuta) and the CCDD species O. latifolia, based on the high level of sequence conservation between the diploid CC genome species and these allotetraploid species. This is the first report of phylogenetic analysis among plant species, based on mitochondrial and chloroplast SSR and their flanking sequences.     

Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae,Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution

Bulbophyllum is the largest genus in Orchidaceae with a pantropical distribution. Due to highly significant diversifications, it is considered to be one of the most taxonomically and phylogenetically complex taxa. The diversification pattern and evolutionary adaptation of chloroplast genomes are poorly understood in this species-rich genus, and suitable molecular markers are necessary for species determination and phylogenetic analysis. A natural Asian section Macrocaulia was selected to estimate the interspecific divergence of chloroplast genomes in this study. Here, we sequenced the complete chloroplast genome of four Bulbophyllum species, including three species from section Macrocaulia. The four chloroplast genomes had a typical quadripartite structure with a genome size ranged from 156,182 to 158,524 bp. The chloroplast genomes included 113 unique genes encoding 79 proteins, 30 tRNAs and 4 rRNAs. Comparison of the four chloroplast genomes showed that the three species from section Macrocaulia had similar structure and gene contents, and shared a number of indels, which mainly contribute to its monophyly. In addition, interspecific divergence level was also great. Several exclusive indels and polymorphism SSR loci might be used for taxonomical identification and determining interspecific polymorphisms. A total of 20 intergenic regions and three coding genes of the most variable hotspot regions were proposed as candidate effective molecular markers for future phylogenetic relationships at different taxonomical levels and species divergence in Bulbophyllum. All of chloroplast genes in four Bulbophyllum species were under purifying selection, while 13 sites within six genes exhibited site-specific selection. A whole chloroplast genome phylogenetic analysis based on Maximum Likelihood, Bayesian and Parsimony methods all supported the monophyly of section Macrocaulia and the genus of Bulbophyllum. Our findings provide valuable molecular markers to use in accurately identifying species, clarifying taxonomy, and resolving the phylogeny and evolution of the genus Bulbophyllum. The molecular markers developed in this study will also contribute to further research of conservation of Bulbophyllum species.     

Plastome phylogenomic analysis of Torreya (Taxaceae)

Torreya Arn., a small genus of Taxaceae, consists of six species occurring in North America and eastern Asia. Several phylogenetic studies have previously been undertaken to reveal relationships within this genus, although only a few DNA segments or species were used. In the present study, we sequenced five Torreya plastomes and combined these with two existing plastomes from the genus to investigate plastome evolution and phylogenetic relationships within Torreya. All sequenced Torreya plastomes shared the same complement of 82 protein‐coding genes, 4 ribosomal RNA genes, and 31 transfer RNA genes. Phylogenetic inference using a maximum likelihood framework consisted of an 82‐gene, 17‐taxon dataset, including all species of Torreya, resolved Torreya as a monophyletic clade. Strongly supported relationships within the genus include the position of the early diverging T. jackii Chun, the two sister pairs T. fargesii Franch.–T. nucifera (L.) Siebold & Zucc. and T. grandis Fortune ex Lindl.–T. californica Torr., and the monophyly of the clade including T. fargesii var. yunnanensis, T. fargesii, and T. nucifera. In addition to the inference of species relationships, divergence time estimation and biogeographical analysis were carried out. The diversification of Torreya was estimated to be approximately 8.9 Ma. Ancestral state reconstruction of the geographical area suggested China/eastern North America as the most likely ancestral region for the six extant Torreya species.     

木犀科植物叶绿体基因组结构特征和系统发育关系

木犀科11属19个种叶绿体基因组的一般特征和变异特征的比较分析显示, 结果表明, 该科叶绿体基因组大小为154-165 kb, 其差异主要是大单拷贝(LSC)长度的差异所致。Jasminum属3个物种的叶绿体基因组长度与其余物种有较大差异, 该属clpP基因内含子和accD基因丢失。共线性分析表明, Jasminum属3个物种多个基因出现基因重排现象, 倒位可能是重排的主要原因。Jasminum属在IRb/SSC和SSC/IRa边界的基因均与其它物种不同; 重复序列与SSR数量检测结果表明, Jasminum属与其余物种在数量及重复长度上差异较大。基于CDS数据构建的系统发育树表明, Abeliophyllum distichum和Forsythia suspensa为木犀科中较早分化的类群。     

Comparative genetic mutation frequencies based on amino acid composition differences

Genetic variation inferred from large-scale amino acid composition comparisons among genomes and chromosomes of several species, Saccharomyces cerevisiae, Drosophila melanogaster, Ceanorhabditis elegans, H. sapiens, is shown to be correlated (highest, r² = 0.9855, p < 0.01) with reported mutation rates for various genes in these species. This study, based largely on pseudogene data, helps to establish reference mutation frequencies that are likely to be representative of overall genome mutation rates in each of the species examined, and provides further insight into heterogeneity of mutation rates among genomes.     

苦马豆叶绿体基因组结构及其特征分析

利用Illumina高通量测序平台对苦马豆（Sphaerophysa salsula）进行测序和组装,获得完整的苦马豆叶绿体基因组序列。组装结果表明,苦马豆叶绿体基因组全长123 327 bp,存在IR区丢失,不具有四分体结构;注释结果显示,苦马豆叶绿体基因组共编码108个基因,其中包含74个蛋白编码基因、4个rRNA基因和30个tRNA基因;叶绿体基因组序列上共检测到99个SSR位点,包含75个单核苷酸、17个二核苷酸和7个三核苷酸重复单元;系统发育分析显示,苦马豆和骆驼刺为姊妹群,亲缘关系最近。这为今后苦马豆遗传多样性、群体遗传结构和物种形成机制研究奠定了基础。